A Deadly Train Ride
by radpineapple
Summary: A train, Agent Scully, the Doctor, and lethal bacteria. That basically sums it up. Image created by the amazing TheMorningTrash on Wattpad.


X-Files Doctor Who Cross-Over

A Deadly Train Ride

A middle-aged man in dark coat and brown fedora hurriedly ran, panting, on a vacant sidewalk late at night. It appeared that he was alone, but he kept running and occasionally looked behind his shoulder. He ran until he arrived at a train station and slowed to brisk walk, trying to look as inconspicuous as possible. He was sweating profusely. He entered the train station and dabbed his face with his handkerchief. He pushed his way to the ticket booth and ignored the annoyed comments and glares.

"I need a ticket please," the man said shoving money into the clerk's face.

She looked annoyed and sighed, "Where are you going?"

"Washington D.C." he replied breathlessly. He looked behind his shoulder again to see if anyone was following him.

The clerk slowly took his money and slid his ticket through the booth.

The man greedily snatched his ticket and made his way to the train. He began coughing very hardly. He put his handkerchief to his mouth while he was coughing, and when he brought it away from his mouth, the handkerchief was speckled with blood mixed with a bright blue liquid. The man was still briskly walking while he was inspecting his handkerchief and he accidentally ran into someone.

The woman he ran into looked very surprised.

"I'm sorry," the man mumbled before he got onto the train.

Agent Dana Scully shook her head as she entered the train right after the man who had just ran into her, unaware that he had accidentally wiped some of the mysterious light blue substance from his handkerchief onto the back of her arm. The substance slowly seeped through her clothing until it was no longer in sight.

O

Agent Scully was sitting in her seat on the train, waiting for it to leave the station. She took out her cell phone, punched in a few numbers, and put it up to her ear.

"Hey, Mulder" she said into the phone. "It's me."

"Hey, Scully!" he replied. "How was your brother's wedding?"

Dana smiled. "It was great. I'm taking the train back to D.C. I'll be there in about twenty-four hours."

"I still don't get why you're taking the train when you could just fly," Mulder said.

"Everything has been so fast-paced lately that this train ride should help slow things down," she said. "Also, it has been a while since I've been on a train. It should be nice."

"Alright," Mulder said. "I'll see you when you get back."

"Bye."

"Bye."

Scully put her phone back into her purse and placed it under her seat. That's when she heard raspy coughing coming from down the aisle. She looked out and saw the man who had bumped into her earlier. He was in one of the seats directly across the aisle from her. His coughing intensified.

"Are you alright, sir?" Scully said to the sweaty, coughing man. He looked quite ill.

"I'm fine thank you," he said, attempting a smile.

The train blew its whistle and began its journey to Washington D.C. Scully looked out her window as the train moved farther away from the station.

O

A few hours later Scully lay asleep in her seat. The coughing man had just finished another round of coughing and looked into his handkerchief; this time it was almost completely covered by the light blue substance. He looked truly distressed. He shakily folded up his handkerchief and put it into his pocket. He looked out the window while wiping his forehead from the sweat that seemed to be incessantly pouring down his face. His breathing became much heavier. He suddenly stood up and began to make his way to the bathroom. He began to cough again, more intensely than ever before. His lungs were too full of fluid, and the coughing wasn't enough to expel the blue substance from his body. He lurched forward, grabbing onto a nearby seat, still coughing. The woman whose seat he had grabbed gave him a dirty look.

"Help me," the man gurgled before falling onto the floor, dead.

The woman screamed.

Scully immediately rushed out of her seat and ran to the scene.

"Everyone back away!" she yelled, gesturing for people to stay back. "I'm a medical doctor!" A man pushed his way through the crowd. He was wearing a light brown trench coat over a brown pinstriped suit. He had messy brown hair and brown, piercing, intelligent eyes. "Sir, you need to stay away," Scully told him.

"I'm a doctor," he said. "I can help."

He knelt down to inspect the man, who lay face down on the floor, and pulled out a small metal instrument with a blue head from the inside pocket of his suit. Scully knelt beside him. The Doctor scanned the dead man with his instrument, which made a peculiar whirring noise. Scully tentatively turned the dead man over and gasped. The light blue substance was seeping out of his mouth, nose, eyes, and ears. People began to panic. The Doctor immediately stood up and pulled Scully away from the dead man.

"Everyone, stay back!" he said.

People began to cry and shout.

"Everyone, stay calm," Scully said. No one listened. "Hey!" she said loudly. People quieted down. She took out her badge, "I'm Special Agent Dana Scully with the FBI. I need all of you to take your belongings and evacuate the car." Everyone obeyed, and soon everyone had left except Agent Scully and the Doctor.

"Nice job getting those people out of the car," the Doctor complimented. "I'm the Doctor, by the way."

Agent Scully nodded. She was too busy looking at the body to respond. "I've never seen anything like this."

"I've heard about it," the Doctor said. "It's very old. I've personally never seen it. There's something I'm forgetting, though," the Doctor said thoughtfully.

"Is it some sort of virus?"

"Bacteria, actually. Although it doesn't originate from here. I wonder how it got on the train," the Doctor paused. "I really do feel like I'm forgetting something about it. That's going to bother me."

"How does it spread?"

"That's it!" the Doctor said. "That's what I forgot! This is quite fascinating, actually. The bacteria lives in this goo," the Doctor said gesturing to the fluid that had escaped through the man's face. "It's a sort of mucus the bacteria creates. It breathes this stuff. Anyway, once the bacteria enter the host, they create as much mucus as they can. Eventually the mucus fills the lungs, causing the host to suffocate, like this man here. Then the bacteria reanimate the body. Then all the bacteria have to do is touch another living body and the process repeats. Brilliant, isn't it?"

Scully looked at him in disbelief. Then she looked at the body, completely terrified. "Reanimate the body?"

"Yup," the Doctor paused, and then looked at the body, "Oh."

The dead man's finger twitched.

"Out!" the Doctor shouted. "Now!"

The Doctor and Agent Scully ran out of the car as the man began to slowly reanimate. The Doctor closed the door behind them and locked it with the metal instrument with the blue head, his sonic screwdriver.

"For the love of all things good and holy," a voice said angrily. "What is going on here?!" The conductor of the train angrily walked down the aisle. People moved out of his way. He angrily walked up to the Doctor and Agent Scully.

"Sir," Agent Scully said showing him her badge. "There are deadly bacteria on this train. We need to stop them before they can spread anymore. You need to stop the train."

The conductor looked at her badge thoughtfully. "What kind of bacteria?"

"Did you not hear her?!" the Doctor said. "The bacteria are deadly! Stop the train so it cannot spread to anymore people!"

A loud banging came from the door behind them. The Doctor and Agent Scully spun around. The dead man could be seen through the small circular window in the door. His eyes were completely blue and his veins could be clearly seen through his skin. They were an unnerving light blue color, most unnatural. Someone screamed.

"I'll stop the train," the conductor said, full of fear. He quickly walked back down the aisle.

The dead man continued to bang on the door. He suddenly stopped. The Doctor and Scully exchanged a look. They slowly approached the car where the dead man resided. They peered through the small, circular window. He was gone. Scully drew her gun and was about to open the door when the Doctor grabbed her arm.

"No guns," he said.

"This thing is dangerous. I will do what I have to do to stop it."

"You can do that without using a gun," the Doctor said stubbornly. "Now put it away."

Scully ignored him and opened the door, cautiously walking in with her gun in her hands, pointing it at the floor.

"He's gone," the Doctor said pointing to an open grate on the ceiling.

Scully put her gun away, "He could be anywhere," she said. The train slowed to a stop. The Doctor and Scully exchanged a look. "It's probably the conductor," Scully said.

"I hope so," the Doctor said taking out his sonic screwdriver. He began to sonic the grate where the dead man had escaped.

"What is that?" Scully said looking at the Doctor's sonic screwdriver.

"Oh, this? It's a sonic screwdriver."

Scully gave him a strange look and opened her mouth as if to ask him something when the lights suddenly flickered off. Someone screamed near the front of the train. The Doctor ran towards it. Scully quickly followed him until she began to cough. She slowed down, but managed to follow the Doctor. They entered the front of the train. The conductor lie wounded on the floor.

"Everyone, stay back!" the Doctor ordered the small crowd that had encircled the conductor. He knelt down next to the conductor and scanned him with his sonic screwdriver. "I'm sorry," the Doctor said to the conductor. "You're dying."

Scully knelt down beside the Doctor. "What's wrong?" Scully asked.

"He was hit in the head," the Doctor explained. "Internal bleeding in the brain. He hasn't got long."

"Can you tell me what happened?" Scully asked the conductor kindly.

"Lead pipe," the conductor said angrily. "I shot 'im, though."

"Who?" the Doctor asked.

"That _thing_ ," the conductor replied. "Whatever it is."

The Doctor and Scully exchanged a look.

"Can you do something for me?" the conductor asked Scully.

"What is it?" she asked.

"Kill 'im. Kill 'im for me." Then the conductor breathed his last.

O

The Doctor and Scully stood outside of the room where the conductor died.

"This makes no sense!" the Doctor said frustratedly. "Why would it kill him?"

"Excuse me," a voice said. A scared looking man came up to Scully and the Doctor. "Are you going to save us?"

Scully was about to reply when the Doctor said to the man, "What's your name?"

"Jacob," he said timidly.

"Yes, Jacob, we are," the Doctor said.

Jacob did not look reassured.

The Doctor put his hands on Jacob's shoulders, "Look at me," the Doctor said. "I promise I will get you out of this."

That seemed to help, and Jacob nodded and returned to his seat.

Scully looked at the Doctor, "Are you sure?" she asked him.

"About what?"

"That you will get him out of this. That you – we, can get anyone out of this."

"Yes I am. Now, the question is, why was the conductor murdered?"

"Do you think someone else killed him?"

"No," the Doctor said. "Look at this lot," he said gesturing to the people in the car before them. Everyone had been moved into the first three cars so it was easier to keep track of everyone. They were all scared and crying or hugging one another. "They're frightened to death," the Doctor said.

Scully looked at the people sadly. Suddenly she had an idea. "How long does it take the bacteria to take over someone's body?"

"A few hours, almost a day, why?"

"Wouldn't it be easier for the bacteria to spread if it just killed its hosts so it wouldn't have to slowly take them over?"

The Doctor caught on to what she was thinking, "You're saying that the bacteria are killing people so they can spread faster." He smiled at Scully. "That's it!"

Scully looked puzzled at the Doctor's amusement.

"We need to find it before it kills anyone else," the Doctor said taking out his sonic screwdriver. "C'mon!" he said before racing down the aisle. Scully coughed into her arm and followed.

O

They slowly walked down the dark aisles of the train with the Doctor's sonic screwdriver leading them towards the bacteria. They stopped in front of the last car.

"It's in here," the Doctor whispered.

Scully drew her gun.

"No," the Doctor said sternly. "That could make it more hostile."

Scully didn't put it away.

"Just this once," the Doctor said.

Scully studied him and then put her gun away. The Doctor opened the door. At first, they could just hear it growling, but then they saw it huddled in the corner. It was clearly wounded. The Doctor edged closer. It growled louder and it grew into a tighter ball. The Doctor stopped.

"Look," he whispered.

Scully saw that it was heavily bleeding the blue mucus from its chest. "The conductor," she whispered.

The Doctor nodded and slowly approached it. He paused, "It won't live long. The mucus is leaving the body too quickly."

Scully quietly coughed.

The Doctor knelt down beside it. It inched away. "Something's wrong," the Doctor said.

"What?"

"This should make it more aggressive than ever. It's dying; it needs to save itself. It needs to find a new host."

It made a wheezing noise. It was laughing.

"Why are you laughing?!" the Doctor said angrily. "You're dying! You need to find a new host! You need to keep your species alive!"

It looked at the Doctor full of amusement. It suddenly began to choke, and then it died.

The Doctor stood up. "We need to burn the body." He left the car. Scully followed.

As they were walking, Scully's vision began to fade. She stumbled.

"Are you alright?" the Doctor said.

Scully cleared her throat, "Yes I'm fine." She walked a few more feet before she passed out.

O

She awoke to the sight of the Doctor scanning her with his sonic screwdriver. She was lying across two seats.

"What's going on?"

The Doctor sat down on one of the seats across from her. "I'm sorry," he said. "I'm so, so sorry."

Scully's blood ran cold. "What's wrong?"

"It was laughing, Scully."

"What was?"

"The bacteria. It was laughing."

Scully was confused.

"It was laughing because it had already spread to someone else," the Doctor explained. "It spread to you, Scully."

She was scared. "How do we stop it? Bacteria can usually be stopped by antibiotics or some form of disinfectant."

The Doctor looked at her thoughtfully, "There technically isn't a cure, but if I was able to…" He suddenly sprang out of his seat. "Stay here!" He raced off. Scully stood up and watched him run down the aisle and into a maintenance cupboard. A few seconds later he came out holding a variety of strange objects. Scully's vision was fading fast. She struggled to keep looking at the Doctor. He scanned her with his sonic screwdriver. He looked nervously at her. "Stay with me," he said touching her arm.

He took out a few bottles full of mysterious liquids and began mixing them together into a red cup. Every few seconds he would look up at her to make sure she was alright.

"Doctor," Scully said, coughing into her arm. She looked at her arm. It was speckled with the blue mucus of the bacteria.

"Hold on!"

Scully began to black out. The Doctor touched her arm. Her eyes focused on him.

"I'm almost done, just stay with me. Keep looking at me," the Doctor said. He mixed in a few more things into the red cup, but Scully couldn't exactly tell what they were because she could hardly focus her vision any more.

"Drink," the Doctor commanded, handing her the red cup.

Agent Scully started to drink it and nearly threw up, but she continued drinking anyway. After she finished, she looked at the Doctor one last time before she fainted.

O

Scully awoke to the sound of people talking. Light streamed through the train windows. She sat up and looked outside. They were at the train station in Washington D.C. Scully was confused. She didn't remember arriving here. She quickly got up and started walking down the aisle. Men and women in hazmat suits were everywhere. They were inspecting the entire train. She didn't see any of the other passengers. Scully was about to leave the train when one of the people in a hazmat suit stopped her.

"I'm sorry, ma'am, but you can't leave," he said gripping her arm.

She jerked it away and pulled out her badge. "I'm with the FBI. What's going on here?" she demanded.

"Agent Dana Scully," he said reading her badge.

"Yes, that's me."

"Go outside. There's someone who wants to see you."

"Who?"

He ignored her and walked away from her towards a group of other hazmats who were inspecting a certain spot on the carpet. She left the train and looked around for whoever wanted to see her. There were men in black suits and wearing pilot shades everywhere. One of them approached her.

"Agent Scully?"

"Yes?"

"Follow me."

"Where am I going? What's going on here?"

"Just follow me, please."

She reluctantly followed him to a black SUV. The Smoking Man stepped out of the car.

"Agent Scully," he said coolly smoking a cigarette. No surprise there.

"Sir, what's going on?"

"I don't know, Agent Scully," he said exhaling a cloud of smoke. "You tell me."

"I think you do know what's going on," she said hotly, "and you're just trying to see what I know."

The Smoking Man took a puff from his cigarette, not showing even a hint of emotion. He then turned to one of the men in black beside him.

"What's the cover story?"

The man warily eyed Agent Scully but replied, "The train was carrying a radioactive element and it leaked. We are containing it right now."

"Radioactive? That seems a bit farfetched," the Smoking Man said harshly.

"If it makes a difference, sir, the teams are picking up radioactive signals. There was something radioactive on this train."

The Smoking Man nodded to him, "That'll be all."

The man glanced at Agent Scully one last time and left.

Scully looked at the Smoking Man in disbelief, "You can't just cover this up! There was something truly dangerous on that train! People need to be aware of it!"

"It has been taken care of, Agent Scully," the Smoking Man replied through a puff of smoke.

"What do you mean?"

"It's none of your concern. Now go home," he said and began to walk away from her.

"What about the Doctor?" she asked. "What have you done to him?"

The Smoking Man paused and turned around. He dropped the cigarette that he had been smoking and crushed it underfoot. "What doctor? Doctor who?" He took out a pack of cigarettes and lit a new one.

Scully realized that she didn't know his name, "I don't know," she said.

"There were no doctors aboard the train besides you, Agent Scully," the Smoking Man said.

Scully was perplexed. "Show me the list of passengers," she commanded.

The Smoking Man stared at her for a second before he whispered to a nearby man in black who quickly retrieved the list of passengers. He handed it to the Smoking Man who looked at it and then handed it to Agent Scully. She took the list. It had the name every passenger and his or her picture next to the name. She didn't see the Doctor on the list anywhere. She checked again. Nothing. She looked up to see the Smoking Man staring at her.

"You're sure these are all of the passengers?"

"I am, Agent Scully."

Suddenly, Scully heard shouts coming from behind her. She spun around. Mulder was pushing his way through men in black who were telling him to stay away.

"I'm Special Agent Fox Mulder! Let me through!" he was saying while waving his badge in front of their faces. They still wouldn't let him pass.

"Let him in," the Smoking Man said to the men in black. They all exchanged a look and then let Mulder through.

"Scully!" he said running towards Agent Scully.

"Mulder!" she replied.

"Are you okay? What happened here?" His eyes settled on the Smoking Man, "What are _you_ doing here?"

"That's none of your business," the Smoking Man said.

"Mulder," Scully said. "We should go."

Mulder looked at the scene before him. The men in black surrounding the train filled with people in hazmat suits. "But, Scully," he said astoundedly.

"C'mon, Mulder," she said grabbing his arm. He looked at her full of astonishment. "I'll explain later," she whispered. Mulder looked back at the scene one last time and then followed Scully to the train station.

O

The Smoking Man silently smoked his cigarette while he watched Agents Mulder and Scully leave. One of the men in black holding a clipboard came up to him.

"Mark this as a level eight," the Smoking Man said.

"But, sir," the man in black replied, "there was hardly any damage done!"

The Smoking Man looked at the other man intently, "Apparently the Doctor was involved."

The man in black nodded vigorously and wrote something down on his clipboard.

"We need to keep our eyes peeled," the Smoking Man said sending smoke into the other man's face. "The Doctor cannot know what we are doing, understood?"

The man in black nodded again and made another note on his clipboard, "Shall I inform the others?"

The Smoking Man thoughtfully smoked his cigarette for a moment and then said, "That would probably be best."

"I'll be right on it, sir," the man with the clipboard said. He hurriedly walked away from the Smoking Man.

The Smoking Man gazed at the train, full in thought, as schemes to keep the Doctor out of his way popped into his head. He took a final puff of his cigarette before he extinguished it and got into his black SUV and drove away.

The End

 **A/N: This is my first time writing X-Files and Doctor Who, and I am a bit timid in posting this. Please tell me what you think. I already have an idea of what I will do for another DW X-Files cross-over if I decide to continue, but that is all up to you guys. I would really appreciate feedback. Thank you all for reading! It means so much to me!**


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